March 2020 - BBClist - maillist.psb.ugent.be

PhD position in Integrating of multiple -omics datasets
by Claesen Jürgen 04 Jun '24

04 Jun '24

Dear all, SCK CEN and UHasselt are looking for candidates for a PhD project with the title: "Integromics - Towards integration of big biomolecular data to enable systems biology" Description The last decades, development of high-throughput technologies such as next-generation sequencing, microarrays and mass spectrometry has led to a paradigm shift in biology and life sciences. Where previously one biomolecule (for example, a gene, or a protein) was studied as a single entity, these experimental techniques allow to study a set of biomolecules (for example, the genome or the proteome) in one go and in a limited amount of time. While, at first, experiments were analyzed independently from each other, combining information of several experimental techniques, and correlating them with environmental and/or clinical parameters, is, nowadays, of great interest. As a consequence, novel statistical and computational methodologies for the analysis of multi-omics datasets have to be developed, allowing a multi-dimensional view on complex biological processes. In this PhD project, we aim at the development of computational methods for the analysis of multi-omics datasets, that are commonly generated by the three biology units of SCK*CEN, which will improve the understanding and valorization of the data, and which will keep the biology units up to date with current developments in biology and bioinformatics. Profile and diploma As a doctorate researcher you will join the dynamic bioinformatics team at SCK CEN and CenStat (UHasselt). A successful candidate should have : * A master degree in biostatistics/applied statistics/bioinformatics/statistical bioinformatics. * You are acquainted with statistical methodologies and had exposure to computer programming in SAS/R/Winbugs/Python. * You can work independently and within a team. * You have excellent communication skills. * You are interested to develop new methodology from both theoretical and applied aspects. * You enjoy working in a multidisciplinary and multicultural environment. * You are willing to closely collaborate with biologists/biostatisticians. * You speak and write English fluently. * You have work experience with at least two different "omics" platforms. For more information contact: Dr. Claesen Jürgen (SCK-CEN), jclaesen(a)sckcen.be<https://academy.sckcen.be/en/Mailform?contactid=b22040b5-cf18-496f-a82a-3bc…> Prof. Shkedy Ziv (Hasselt University), ziv.shkedy(a)uhasselt.be<https://academy.sckcen.be/en/Mailform?contactid=51ae7733-8006-4347-b211-9a4…> Link to the project in SCK-CEN: https://academy.sckcen.be/en/Your_thesis_internship/AllTopics/Integromics--… Kind Regards, Jürgen

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NERC Bursaries for Edinburgh Genomics Courses
by TRAIN edgenomics-training 02 Mar '22

02 Mar '22

Dear All We are pleased to announce we have a number of bursaries available to cover up-to the full fees of any of our upcoming bioinformatics courses. These bursaries are available to UK based students or researchers funded by the NERC or working on research that falls under the remit of the NERC (https://nerc.ukri.org/research/portfolio/remit/) Bursaries are available for any of our courses (see below) but are available for a LIMITED TIME ONLY: They are available for any course booked BEFORE 27th MARCH. So please don't wait to sign up! Our upcoming courses: Linux for Genomics, 13th March - An introduction to working on the command line, running commands and handling data relevant to bioinformatics. https://genomics.ed.ac.uk/services/linux-genomics R for Genomics, 14-15th March - An introduction to the statistical environment R, taking you from the very basics to writing basic functions and creating beautiful figures with ggplot2 https://genomics.ed.ac.uk/services/r-genomics Introduction to Python for Biologists, 18-22 March - This introductory course gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. https://genomics.ed.ac.uk/services/introduction-python-biologists-0 Data Manipulation and Visualisation with Python, 08 - 12 April - Python has a many high-quality libraries for working with scientific data. In this workshop we will see how to leverage these libraries to efficiently work with and visualise large volumes of data. https://genomics.ed.ac.uk/services/data-manipulation-and-visualisation-pyth… Introduction to RNA-seq Data Analysis, 9-10th May - This two-day course takes you through a tried-and-tested workflow for analysing RNA-seq data, from read mapping and QC to differential expression and result visualisation. https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis If you think you are provably eligible for one of these bursaries, sign up to your desired course through the link provided and we will be in contact regarding fees. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics G.06, Ashworth Laboratories, Charlotte Auerbach Road, The King's Buildings, The University of Edinburgh, EH9 3FL, Edinburgh, Scotland Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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The Swedish Elixir node is looking for 1--2 Data Stewards
by Bengt Persson 31 Mar '20

31 Mar '20

Dear all, The Swedish Elixir node is looking for a Data Steward. Deadline is 20 April. More details are available at: https://uu.se/en/about-uu/join-us/details/?positionId=320306 All the best, Yours, Bengt Persson Head of Node Elixir-SE -- Bengt Persson, M.D., Ph.D. Professor of Bioinformatics Director of NBIS (National Bioinformatics Infrastructure Sweden) Science for Life Laboratory Uppsala University & Karolinska Institutet Telephone: +46 18 471 4422 Mobile phone: +46 70 425 0230 Facsimile: +46 18 530 396 E-mail: bpn(a)icm.uu.se<mailto:bpn@icm.uu.se>, bpn(a)nbis.se<mailto:bpn@nbis.se>, bengt.persson(a)ki.se<mailto:bengt.persson@ki.se> Addresses: Uppsala University | Karolinska Institutet SciLifeLab | SciLifeLab ICM -- Department of | MBB -- Department of Medical Cell and Molecular Biology | Biochemistry and Biophysics BMC, room C10:308c | House Gamma, level 6, G6613 Box 596 | Box 1031 S-751 24 Uppsala, SWEDEN | S-171 21 Stockholm, SWEDEN När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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online open Software Carpentry workshop on April 14-17
by Mateusz Kuzak 31 Mar '20

31 Mar '20

Dear all, The Netherlands eScience Center is organising a Software Carpentry workshop on April 14-17. As a consequence of the social distancing measures applied to counteract the covid-19 spread, we have decided to host the workshop entirely online. To accommodate parents and those taking care of their families or having other responsibilities, we decided to spread out the workshop over four consecutive mornings. The workshop covers (i) introduction to Unix shell, (ii) version control with git and collaboration on GitHub, (iii) introduction to exploratory data analysis in Python with the use of Jupyter notebooks. The workshop is free of charge, but it is limited to 20 participants (first come, first served). Please find the schedule and more information on the workshop website and register via the Eventbrite. kind regards, Mateusz

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2 phd positions @BIOBIX, Ghent University
by Tim De Meyer 30 Mar '20

30 Mar '20

Dear colleagues, please find in attach 2 vacancies for bioinformaticians / omics data analists @ the BIOBIX lab of Ghent University, focusing on allele-specific studies in big RNA-seq data (100s of samples), one in the medical (cancer) and one in the applied biological (herbivore adaptation to novel hosts as well as pesticides) fields. Please distribute within your network & to potentially interested students. Best regards, Tim De Meyer Associate Professor BIOBIX Lab. of Bioinformatics and Computational Genomics BIG N2N & CRIG Dept. Data Analysis & Mathematical Modelling Faculty of Bioscience Engineering - Ghent University - Belgium Tim.DeMeyer(a)UGent.be +3292645987 www.biobix.be <http://www.biobix.be/> https://scholar.google.be/citations?user=OrDlWKsAAAAJ

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PhD position - lettuce bioinformatics
by Smit, Sandra 30 Mar '20

30 Mar '20

The Bioinformatics Group at Wageningen University is looking for a PhD student on lettuce pangenomics, as part of a large research program, LettuceKnow. Are you skilled in plant bioinformatics, interested in the combination of method development and genome analysis, and eager to collaborate with experimental plant biologists? This may be the right position for you. Full description at: https://www.wur.nl/en/vacancy/PhD-Student-Lettuce-Pangenomics.htm Kind regards, Sandra Smit ---- Dr. Sandra Smit Assistant Professor Bioinformatics, Wageningen University Email: Sandra.Smit(a)wur.nl<mailto:Sandra.Smit@wur.nl> ----

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Utrecht Uni vacancies: Bioinformatician; PhD student Viromics
by Bas E. Dutilh 28 Mar '20

28 Mar '20

Dear colleagues, I hope that everything is OK with you all in terms of health and working from home. Here, the work continues from home and I am currently looking for two new colleagues to strengthen the Utrecht University Metagenomics Group: 1) *Bioinformatician / Data Steward for Metagenomics*: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/bioinf… 2) *PhD student Viral Metagenomics for One Health*: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-po… Please forward this message to potential candidates. You could also consider retweeting: Bioinformatician: https://twitter.com/BEDutilh/status/1243874743813648384 PhD student Viromics: https://twitter.com/BEDutilh/status/1243873143472652289 Kind regards, Bas -- Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Metagenomics Group <https://wiki.ubc.uu.nl/mgx/> Theoretical Biology and Bioinformatics <http://tbb.bio.uu.nl/>, Utrecht University <https://www.uu.nl> Utrecht Bioinformatics Center <https://ubc.uu.nl/> +31 (0)30 253 4212

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Fwd: [ifb-all] 31 MAI : Direction du Hub de Bioinformatique et Biostatistique de l’Institut Pasteur
by Jacques van Helden 28 Mar '20

28 Mar '20

Dear colleagues, The Institut Pasteur in Paris is recruiting a Director for the Bioinformatics Hub. The application deadline has been postponed to May 31. Please don't hesitate to forward the following announcement. Best regards, Jacques van Helden Institut Français de Bioinformatique (IFB) http://www.france-bioinformatique.fr French node of the European ELIXIR bioinformatics infrastructure https://elixir-europe.org/about-us/who-we-are/nodes/france Jacques.vanHelden(a)france-bioinformatique.fr https://orcid.org/0000-0002-8799-8584 ============ Begin forwarded message: From: "Olivier GASCUEL" <olivier.gascuel(a)pasteur.fr> Subject: [ifb-all] 31 MAI : Direction du Hub de Bioinformatique et Biostatistique de l’Institut Pasteur Date: 28 March 2020 at 10:48:48 CET To: "ifb-all(a)groupes.france-bioinformatique.fr" <ifb-all(a)groupes.france-bioinformatique.fr> Reply-To: "Olivier GASCUEL" <olivier.gascuel(a)pasteur.fr> Bonjour à tous, J’espère que tout va bien pour vous et vos proches. Ce mail pour signaler que nous avons repoussé au 31 Mai la date limite pour déposer un dossier pour la Direction du Hub de l’Institut à Pasteur, cf. ci-dessous. A une « prochaine », bien amicalement, Olivier Gascuel MERCI DE DIFFUSER CE MAIL !! CHANGEMENT DE DATE LIMITE : 31 MAI 2020 Direction du Hub de Bioinformatique et Biostatistique de l’Institut Pasteur https://research.pasteur.fr/fr/team/bioinformatics-and-biostatistics-hub/ Le Hub de Bioinformatique et Biostatistique de l’Institut Pasteur, lancé en 2015, regroupe cinquante ingénieurs de recherche. Trente appartiennent au Hub Core et travaillent essentiellement sur les projets déposés par les Unités de recherche de l’institut. Vingt sont mis à disposition des Unités et Plateformes pour des périodes longues, mais conservent une affiliation à 20% au Hub pour la formation, les échanges et l’animation scientifique. Le Hub est une composante du Département de Biologie Computationnelle de l’Institut Pasteur (C3BI jusqu’en 2019, USR 3756 avec le CNRS - Directeur Olivier Gascuel). Le Hub est structuré en sept pôles experts (web, algorithmique et programmation, statistique, génomique, régulation, phylogénétique, biologie des systèmes). Les projets traités sont très divers en durée (de quelques jours à plusieurs années) comme en nature (analyses de données, bases de données, logiciels, interfaces et serveurs web, etc.). Près de 400 projets ont été traités par le Hub depuis sa création, ayant donné lieu à plus de 150 publications dont certaines dans Nature, Science ou PNAS. Le Hub a également une mission de formation (doctorants, chercheurs, réseau international) et il prend une part active dans la vie du Département de Biologie Computationnelle (séminaires, projets collaboratifs, retraite annuelle). L’Institut Pasteur recherche un/une Directeur/Directrice pour le Hub, avec un fort profil : * Haut niveau scientifique et reconnaissance internationale en bioinformatique et/ou biostatistique. * Expérience démontrée dans la gestion de plateformes de bioinformatique. * Capacité et motivation pour gérer l’ensemble du Hub et pour manager l’équipe (forte charge RH, recrutements, détachements, évolution des carrières, projets nombreux, facturation des services, enseignement et formation, animation et structuration scientifique...). * Capacité à jouer un rôle moteur dans l’évolution du Hub (veille technologique, formation permanente des personnels, transformations des modes de fonctionnement et de gestion des projets…). * Capacité à interagir avec les instances clefs de l’Institut Pasteur (Direction, DSI, Départements scientifiques, Plateformes, Centre Nationaux de Référence (CNR)...) et avec le Département de Biologie Computationnelle et ses Unités de recherche. * Capacité à assurer les liens avec les structures nationales (IFB, France Génomique, AVIESAN…) et internationales (ELIXIR) de bioinformatique. Au-delà de ces tâches et fonctions, le/la Directeur/Directrice du Hub sera encouragé/e à développer des activités propres de recherche et développement en relation étroite avec le campus et ses besoins, en mettant en place un nouveau pôle expert au sein du Hub. Seront notamment favorisés les thèmes liés : aux bases de données et de connaissance biomédicales ; à l’analyse, au partage, à la protection et la valorisation de ces données et connaissances ; à la science des données et à l’intelligence artificielle et leurs applications en biologie-santé. Il/elle aura sur ce thème une expertise reconnue et sera un point focal pour l’institut pour tout ce qui touche à la thématique. Il/elle assurera avec les ingénieurs de son pôle la mise en place de programmes, systèmes et infrastructures (en lien avec la DSI) bénéficiant au plus grand nombre au sein de l’institut et dans le réseau international. Pour candidater, envoyer à mona.ramadan(a)pasteur.fr avant le 31/05/2020 (document pdf unique, caractères 11 points minimum, interligne 14 points minimum) : (1) Résumé de la candidature, 1 page maximum ; (2) CV détaillé, 4 pages maximum ; (3) Motivations et projets pour le poste, 5 pages maximum ; (4) Liste de publications, brevets, logiciels et bases de données ; (5) Coordonnées de référents que nous pourrons contacter pour obtenir des avis sur la candidature. Contacts : mona.ramadan(a)pasteur.fr (RH), olivier.gascuel(a)pasteur.fr (Directeur Dpt.) MERCI DE DIFFUSER CE MAIL !!

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ECCB2020 - Submission deadlines extended for Highlights, Proceedings and Applications
by Eva Alloza 25 Mar '20

25 Mar '20

/- Apologies for multiple posting -/ Dear colleagues, *ECCB2020 submission deadlines ***have been extended *for the highlights, proceedings and applications tracks.* Please consider submitting your contributions and helping us sharing the below mailing among your contacts. Best regards, Eva Alloza, on behalf of the ECCB Organizing Commitee -- Eva Alloza Training and Support Officer Spanish National Bioinformatics Institute (INB) mail: eva.alloza(a)bsc.es phone: +34 934017139 web: http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) c/Jordi Girona, 31 - Torre Girona Building 08034 Barcelona (Spain) ------------------------------------------------------------------------ Merge Doc View this email in your browser <http://mail.eventsairmail.com/ls/click?upn=uJGsKvA4CvNznJb2JMu3nKQ5Z-2FU08S…> <http://mail.eventsairmail.com/ls/click?upn=uJGsKvA4CvNznJb2JMu3nGV2ZgR2xugF…> Submission deadline extended! Call for Highlights, Proceedings and Applications If you had missed the previous deadline, now is the time to submit your contributions! <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> Highlights <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86GyIs3RJaME8…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> Proceedings < https://eccb2020.info/call-for-proceedings/> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86GyIs3RJaME8…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> Applications <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86GyIs3RJaME8…> ------------------------------------------------------------------------ <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…><http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> *Call for Posters* /Deadline: June 4th, 2020 / Remember! Call for posters is still open. You can send your poster until June 4th, 2020 -- Submit today <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86Bu8lyRk-2Bb…> www.eccb20.org <http://mail.eventsairmail.com/ls/click?upn=uJGsKvA4CvNznJb2JMu3nGV2ZgR2xugF…> <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86N7WOuYfIwMj…>#ECCB2020 <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> TECHNICAL SECRETARIAT Ph. + 34 93 882 38 78 eccb2020(a)bcocongresos.com <mailto:eccb2020@bcocongresos.com> www.bcocongresos.com <http://mail.eventsairmail.com/ls/click?upn=vTVo9WAROVynOTbDemV86IZ8Vkhn8oIW…> View this email in your browser <http://mail.eventsairmail.com/ls/click?upn=uJGsKvA4CvNznJb2JMu3nKQ5Z-2FU08S…> http://bsc.es/disclaimer

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PhD position - lettuce bioinformatics
by Smit, Sandra 17 Mar '20

17 Mar '20

The Bioinformatics Group at Wageningen University is looking for a PhD student on lettuce pangenomics, as part of a large research program, LettuceKnow. Are you skilled in plant bioinformatics, interested in the combination of method development and genome analysis, and eager to collaborate with experimental plant biologists? This may be the right position for you. Full description at: https://www.wur.nl/en/vacancy/PhD-Student-Lettuce-Pangenomics.htm Kind regards, Sandra Smit ---- Dr. Sandra Smit Assistant Professor Bioinformatics, Wageningen University Email: Sandra.Smit(a)wur.nl<mailto:Sandra.Smit@wur.nl> ----

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